Alpha-diversity

Where we analyse the effect of a factor on local diversity

Author: Adrien Taudière

Date: October 21, 2024

Code

library(knitr)
library(targets)
library(MiscMetabar)

Code

#d_pq <- tar_read(script=here::here("_targets.R"))
d_pq <- data_fungi

Code

hill_pq(data_fungi, params$factor_of_interest, one_plot = TRUE)

Taxa are now in rows.

2 out of 3 Hill scales do not show any global trends with you factor Time. Tuckey HSD plot is not informative for those Hill scales. Letters are not printed for those Hill scales

Citation

BibTeX citation:

@online{taudière2024,
  author = {Taudière, Adrien},
  title = {Alpha-Diversity},
  date = {2024-10-21},
  langid = {en}
}

For attribution, please cite this work as:

Taudière, Adrien. 2024. “Alpha-Diversity.” October 21, 2024.

---
title: "Alpha-diversity"
subtitle: "Where we analyse the effect of a factor on local diversity"
date: last-modified
author:
  - name: Adrien Taudière
    url: https://adrientaudiere.github.io/bioinfo.starter/analylis/02_alpha_diversity.qmd
    affiliation: IdEst
    affiliation-url: https://orcid.org/my-orcid?orcid=0000-0003-1088-1182
citation: true
# bibliography: bibliography.bib
# link-citations: true
params: 
  factor_of_interest: "Time"
---

# Needed when work interactively


```{r,  message=FALSE, warning=FALSE}
library(knitr)
library(targets)
library(MiscMetabar)
```

```{r}
#| echo: false
#| include: false
params <- rmarkdown::yaml_front_matter(here::here("analylis/02_alpha_diversity.qmd"))$params
```

```{r}
#d_pq <- tar_read(script=here::here("_targets.R"))
d_pq <- data_fungi
```


```{r}
hill_pq(data_fungi, params$factor_of_interest, one_plot = TRUE)
```